The visitors took an early lead with just 2 minutes on the clock through Conor McCarthy.
Waterford brougtht the game level on 51 minutes when Cork skipper Conor McCormack put the ball into his own net while trying to clear a Gavin Holohan cross.
The home side sealed the victory in the 81st minute after Courteney Duffus finished an Izzy Akinade attempt on goal.
Four players, Waterford's Bastien Héry and Stanley Aboah and Cork's Garry Buckley and Steven Beattie, as well as both managers were sent off in the dying minutes of the game after a bizarre touchline row exploded.
However it made no difference to the full time result, as it finished Waterford FC 2 Cork City 1.
The Blues now sit joint top of the Airtricity League Premier Division for the first time in many years.
